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- PDB-5fiy: crystal structure of coiled coil domain of PAWR -

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Basic information

Entry
Database: PDB / ID: 5fiy
Titlecrystal structure of coiled coil domain of PAWR
ComponentsPRKC APOPTOSIS WT1 REGULATOR PROTEIN
KeywordsAPOPTOSIS
Function / homology
Function and homology information


positive regulation of relaxation of smooth muscle / positive regulation of hindgut contraction / positive regulation of neutrophil extravasation / positive regulation of hydrogen peroxide-mediated programmed cell death / cellular response to vitamin E / leucine zipper domain binding / positive regulation of amyloid precursor protein biosynthetic process / positive regulation of neuronal action potential / positive regulation of leukocyte tethering or rolling / negative regulation of calcium ion import ...positive regulation of relaxation of smooth muscle / positive regulation of hindgut contraction / positive regulation of neutrophil extravasation / positive regulation of hydrogen peroxide-mediated programmed cell death / cellular response to vitamin E / leucine zipper domain binding / positive regulation of amyloid precursor protein biosynthetic process / positive regulation of neuronal action potential / positive regulation of leukocyte tethering or rolling / negative regulation of calcium ion import / positive regulation of action potential / cellular response to follicle-stimulating hormone stimulus / protein phosphatase 1 binding / activation of cysteine-type endopeptidase activity / response to iron(II) ion / negative regulation of T cell receptor signaling pathway / negative regulation of B cell proliferation / detection of temperature stimulus involved in sensory perception of pain / positive regulation of phosphoprotein phosphatase activity / actin filament bundle assembly / calcium ion import across plasma membrane / cellular response to interleukin-1 / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of T cell proliferation / negative regulation of fibroblast proliferation / cellular response to estradiol stimulus / apoptotic signaling pathway / protein kinase C binding / response to wounding / positive regulation of cellular senescence / positive regulation of neuron apoptotic process / response to estradiol / actin binding / response to lipopolysaccharide / neuron projection / positive regulation of apoptotic process / axon / negative regulation of gene expression / neuronal cell body / apoptotic process / positive regulation of gene expression / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Prostate apoptosis response 4
Similarity search - Domain/homology
: / PRKC apoptosis WT1 regulator protein
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsTiruttani Subhramanyam, U.K. / Kubicek, J. / Eidhoff, U.B. / Labahn, J.
CitationJournal: Cell Death Differ. / Year: 2017
Title: Structural basis for the regulatory interactions of proapoptotic Par-4.
Authors: Tiruttani Subhramanyam, U.K. / Kubicek, J. / Eidhoff, U.B. / Labahn, J.
History
DepositionOct 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
B: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
C: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
D: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
E: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
F: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
G: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,51325
Polymers86,8107
Non-polymers70418
Water48627
1
A: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
B: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0378
Polymers24,8032
Non-polymers2356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
D: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0769
Polymers24,8032
Non-polymers2747
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
F: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
G: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8814
Polymers24,8032
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
hetero molecules

E: PRKC APOPTOSIS WT1 REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0378
Polymers24,8032
Non-polymers2356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 114.990, 121.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9872, 0.0429, 0.1534), (0.0149, 0.9837, -0.1791), (-0.1586, -0.1745, -0.9718)293.4857, 11.7839, 177.5862
3given(-0.7306, -0.6826, -0.0176), (0.6825, -0.7308, 0.0087), (-0.0188, -0.0057, 0.9998)266.9137, -116.1111, -17.5204
4given(0.7543, 0.6556, 0.0337), (0.6515, -0.7412, -0.1621), (-0.0813, 0.1442, -0.9862)34.4592, -94.5381, 188.9183
5given(0.7047, 0.7042, -0.0869), (-0.6992, 0.71, 0.0833), (0.1204, 0.0021, 0.9927)81.0921, 88.9706, -27.8389
6given(0.989, 0.131, 0.0682), (0.1411, -0.9744, -0.1749), (0.0435, 0.1826, -0.9822)24.145, 16.0761, 142.4849
7given(-0.9733, -0.1084, -0.2021), (0.1123, -0.9936, -0.0078), (-0.2, -0.0303, 0.9793)292.2106, 7.9236, 29.2294

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Components

#1: Protein
PRKC APOPTOSIS WT1 REGULATOR PROTEIN / PROSTATE APOPTOSIS RESPONSE 4 PROTEIN / PAR-4 / TRANSCRIPTIONAL REPRESSOR PAR-4-LIKE PROTEIN PAWR


Mass: 12401.384 Da / Num. of mol.: 7 / Fragment: COILED COIL DOMAIN, UNP RESIDUES 240-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q62627
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 % / Description: DATA STATS ARE FROM HIGH ENERGY REMOTE
Crystal growpH: 5.9 / Details: 100 MM SODIUM CITRATE PH 5.9, 42% TERTIARY BUTANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9770, 0.9794, 0.9795, 0.9825
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
20.97941
30.97951
40.98251
ReflectionResolution: 3→53.82 Å / Num. obs: 16918 / % possible obs: 99.7 % / Redundancy: 9 % / Biso Wilson estimate: 73.24 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 3→3.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD
Starting model: BACKBONE MODEL FROM SHELXE

Resolution: 3→41.809 Å / SU ML: 0.48 / σ(F): 1.79 / Phase error: 33.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2944 3017 9.7 %
Rwork0.2454 --
obs0.2502 16862 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→41.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 18 27 3878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053916
X-RAY DIFFRACTIONf_angle_d0.815228
X-RAY DIFFRACTIONf_dihedral_angle_d13.9951649
X-RAY DIFFRACTIONf_chiral_restr0.032607
X-RAY DIFFRACTIONf_plane_restr0.003702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.04690.40511540.27751281X-RAY DIFFRACTION100
3.0469-3.09690.39651370.30211274X-RAY DIFFRACTION100
3.0969-3.15020.42251230.31061290X-RAY DIFFRACTION100
3.1502-3.20750.38741470.30091265X-RAY DIFFRACTION100
3.2075-3.26920.34431310.28231303X-RAY DIFFRACTION100
3.2692-3.33590.3151490.27741271X-RAY DIFFRACTION100
3.3359-3.40840.30141380.24341275X-RAY DIFFRACTION100
3.4084-3.48760.31681360.24161297X-RAY DIFFRACTION100
3.4876-3.57480.34981450.26251262X-RAY DIFFRACTION100
3.5748-3.67140.37851370.26341267X-RAY DIFFRACTION100
3.6714-3.77940.33071210.27341294X-RAY DIFFRACTION100
3.7794-3.90130.30521430.21011278X-RAY DIFFRACTION100
3.9013-4.04060.24721290.19231277X-RAY DIFFRACTION100
4.0406-4.20220.25311320.20381294X-RAY DIFFRACTION100
4.2022-4.39330.22981410.21541283X-RAY DIFFRACTION100
4.3933-4.62460.25711300.21971287X-RAY DIFFRACTION100
4.6246-4.9140.32961430.2361288X-RAY DIFFRACTION100
4.914-5.29270.25451320.23581285X-RAY DIFFRACTION100
5.2927-5.8240.34581300.29761285X-RAY DIFFRACTION100
5.824-6.66390.37841390.29231278X-RAY DIFFRACTION100
6.6639-8.38460.26371410.24571281X-RAY DIFFRACTION100
8.3846-41.81270.24191390.24611202X-RAY DIFFRACTION94

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